import_pose.cc File Reference

various functions to construct Pose object(s) from PDB(s) More...

#include <core/import_pose/import_pose.hh>
#include <core/import_pose/FullModelPoseBuilder.hh>
#include <core/import_pose/import_pose_options.hh>
#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/VariantType.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/carbohydrates/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/util/metalloproteins_util.hh>
#include <core/pack/pack_missing_sidechains.hh>
#include <core/pack/optimizeH.hh>
#include <core/io/pdb/pdb_reader.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/pose_from_sfr/PoseFromSFRBuilder.hh>
#include <core/io/mmcif/cif_reader.hh>
#include <core/io/mmtf/mmtf_reader.hh>
#include <core/io/StructFileRep.hh>
#include <core/fragment/rna/RNA_MatchType.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/id/TorsionID.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/magnesium.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <cifparse/CifFile.h>
#include <cifparse/CifParserBase.h>
#include <tuple>
#include <boost/algorithm/string/predicate.hpp>
#include <core/pose/full_model_info/FullModelParameters.hh>
#include <utility/stream_util.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::import_pose

Typedefs
using	CifFileOP = utility::pointer::shared_ptr< CifFile >
using	CifParserOP = utility::pointer::shared_ptr< CifParser >

Functions
static basic::Tracer	TR ("core.import_pose.util")
static basic::Tracer	core::import_pose::TR ("core.import_pose.import_pose")
std::ostream &	core::import_pose::operator<< (std::ostream &stream, FileType type)
std::string	core::import_pose::extension_from_filetype (FileType const filetype)
	Given a filetype, return the string for the extension. More...
void	core::import_pose::read_all_poses (utility::vector1< std::string > const &filenames, utility::vector1< core::pose::PoseOP > &poses)
void	core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, io::StructFileRepCOP, bool read_fold_tree)
void	core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, ImportPoseOptions const &options, bool read_fold_tree)
pose::PoseOP	core::import_pose::pose_from_file (std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
	Returns a PoseOP object from the Pose created from input PDB <filename> More...
pose::PoseOP	core::import_pose::pose_from_file (std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
	Returns a PoseOP object from the Pose created from input PDB <filename>, taking a set of custom ImportPoseOptions parameters. More...
pose::PoseOP	core::import_pose::pose_from_file (chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
	Returns a PoseOP object from the Pose created by reading the input PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
FileType	core::import_pose::determine_file_type (std::string const &contents_of_file)
	Determine what file type is passed to function there should only be one function that calls this, pose_from_file and only calls it when the filetype is unknown. More...
void	core::import_pose::pose_from_file (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType file_type)
void	core::import_pose::pose_from_file (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
	Reads in data from input PDB <filename> and stores it in the Pose <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
void	core::import_pose::pose_from_file (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
	Reads in data from input PDB <filename> and stores it in the Pose <pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default. More...
void	core::import_pose::pose_from_file (pose::Pose &pose, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
utility::vector1< core::pose::PoseOP >	core::import_pose::poseOPs_from_files (utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
utility::vector1< core::pose::PoseOP >	core::import_pose::poseOPs_from_files (utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
utility::vector1< core::pose::Pose >	core::import_pose::poses_from_files (utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
utility::vector1< core::pose::Pose >	core::import_pose::poses_from_files (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
utility::vector1< core::pose::PoseOP >	core::import_pose::poseOPs_from_files (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
void	core::import_pose::pose_from_file (utility::vector1< pose::Pose > &poses, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
	Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using the FA_STANDARD ResidueTypeSet (fullatom) More...
void	core::import_pose::pose_from_file (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
	Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using ResidueTypeSet <residue_set> More...
void	core::import_pose::pose_from_file (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
void	core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, ImportPoseOptions const &options, std::string const &filename)
void	core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, std::string const &filename)
void	core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
void	core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options, std::string const &filename)
void	core::import_pose::pose_from_pdb_stream (pose::Pose &pose, std::istream &pdb_stream, std::string const &filename, ImportPoseOptions const &options)
void	core::import_pose::centroid_pose_from_pdb (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false)
	Reads in data from input PDB <filename> and stores it in the Pose <pose> using the CENTROID ResidueTypeSet (centroid) More...
void	core::import_pose::build_pose (io::StructFileRepOP fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set)
	Create pose object, using given StructFileRep object. If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line. More...
void	core::import_pose::build_pose (io::StructFileRepOP fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
	Build Rosetta 3 Pose object from StructFileRep. More...
void	core::import_pose::build_pose_as_is (io::StructFileRepOP sfr, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
	Try to Build pose object from pdb 'as-is'. PDB file must be really clean. More...
void	core::import_pose::build_pose_as_is2 (io::StructFileRepCOP, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, ImportPoseOptions const &options)
pose::PoseOP	core::import_pose::initialize_pose_and_other_poses_from_command_line (core::chemical::ResidueTypeSetCOP rsd_set)
PoseOP	core::import_pose::initialize_pose_and_other_poses_from_options (core::chemical::ResidueTypeSetCOP rsd_set, utility::options::OptionCollection const &options)
PoseOP	core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses (core::chemical::ResidueTypeSetCOP rsd_set, utility::options::OptionCollection const &options, utility::vector1< pose::PoseOP > &input_poses)
void	core::import_pose::get_other_poses (utility::vector1< pose::PoseOP > &other_poses, utility::vector1< std::string > const &other_files, core::chemical::ResidueTypeSetCOP rsd_set)
core::pose::PoseOP	core::import_pose::get_pdb_with_full_model_info (std::string const &input_file, core::chemical::ResidueTypeSetCOP rsd_set)
core::pose::PoseOP	core::import_pose::get_pdb_and_cleanup (std::string const &input_file)
core::pose::PoseOP	core::import_pose::get_pdb_and_cleanup (std::string const &input_file, core::chemical::ResidueTypeSetCOP rsd_set)
void	core::import_pose::cleanup (pose::Pose &pose, bool const force_cut_at_rna_chainbreak)
FullModelParametersOP	core::import_pose::get_sequence_information (std::string const &fasta_file, vector1< Size > &cutpoint_open_in_full_model, bool const append_virtual)
void	core::import_pose::setup_for_density_scoring (core::pose::Pose &pose)
vector1< Size >	core::import_pose::get_cutpoints_from_numbering (vector1< core::sequence::SequenceCOP > const &fasta_sequences, vector1< char > const &conventional_chains, vector1< std::string > const &conventional_segids, vector1< int > const &conventional_numbering)
void	core::import_pose::get_extra_cutpoints_from_names (Size const nres, vector1< Size > &cutpoints, std::map< Size, std::string > const &non_standard_residue_map)
vector1< Size >	core::import_pose::get_cutpoints (vector1< core::sequence::SequenceCOP > const &fasta_sequences, std::map< Size, std::string > const &non_standard_residue_map, vector1< char > const &conventional_chains, vector1< int > const &conventional_numbering, vector1< std::string > const &conventional_segids)
void	core::import_pose::setup_water_bank_for_magnesiums (std::map< Size, std::string > &non_standard_residue_map, vector1< core::sequence::SequenceOP > &fasta_sequences)
void	core::import_pose::look_for_dna (vector1< core::sequence::SequenceOP > &fasta_sequences)
void	core::import_pose::setup_fold_trees (vector1< Pose * > &pose_pointers, vector1< Size > &cutpoint_open_in_full_model, vector1< Size > &fixed_domain_map, vector1< Size > const &cutpoint_closed, vector1< Size > const &extra_minimize_res, vector1< Size > const &extra_minimize_jump_res, vector1< Size > const &sample_res, vector1< Size > const &working_res, vector1< Size > const &jump_res, vector1< Size > const &preferred_root_res, vector1< Size > const &virtual_sugar_res, FullModelParameters const &full_model_parameters, vector1< vector1< Size > > const &pose_res_lists)
void	core::import_pose::update_pose_fold_tree (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &extra_min_res, vector1< Size > const &sample_res, vector1< Size > const &jump_res, core::pose::full_model_info::FullModelParameters const &full_model_parameters)
void	core::import_pose::define_chains (pose::Pose const &pose, vector1< vector1< Size > > &all_res_in_chain, vector1< vector1< Size > > &all_fixed_res_in_chain, vector1< Size > const &res_list, vector1< Size > const &moveable_res)
void	core::import_pose::setup_user_defined_jumps (vector1< Size > const &jump_res, vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< pair< Size, Size > > &chain_connections, vector1< Size > const &res_list, vector1< vector1< Size > > const &all_res_in_chain)
Size	core::import_pose::get_chain (Size const i, vector1< vector1< Size > > const &all_res_in_chain)
void	core::import_pose::setup_jumps (core::pose::Pose const &pose, vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< pair< Size, Size > > &chain_connections, vector1< vector1< Size > > const &all_res_in_chain, std::tuple< vector1< int >, vector1< char >, vector1< std::string > > const &resnum_and_chain_and_segid_in_pose)
FoldTree	core::import_pose::get_tree (pose::Pose const &pose, vector1< Size > const &cuts, vector1< Size > const &jump_partners1, vector1< Size > const &jump_partners2)
FoldTree	core::import_pose::get_tree (Size const nres, vector1< Size > const &cuts, vector1< Size > const &jump_partners1, vector1< Size > const &jump_partners2, vector1< std::string > const &jump_atoms1, vector1< std::string > const &jump_atoms2)
void	core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs (utility::vector1< Size > &fixed_domain, pose::Pose const &pose, utility::vector1< Size > const &res_list, utility::vector1< pair< Size, Size > > const &extra_minimize_jump_pairs)
void	core::import_pose::update_fixed_domain_from_extra_minimize_jump_res (vector1< Size > &fixed_domain, pose::Pose const &pose, vector1< Size > const &res_list, vector1< Size > const &extra_minimize_jump_res)
void	core::import_pose::add_cutpoint_closed (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &cutpoint_closed)
void	core::import_pose::put_in_cutpoint (pose::Pose &pose, Size const i)
void	core::import_pose::add_virtual_sugar_res (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &virtual_sugar_res)
utility::vector1< Size >	core::import_pose::figure_out_working_res (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &sample_res)
utility::vector1< Size >	core::import_pose::figure_out_sample_res (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &working_res)
void	core::import_pose::check_working_res (utility::vector1< Size > const &working_res, utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &sample_res)
void	core::import_pose::figure_out_motif_mode (utility::vector1< Size > &extra_min_res, utility::vector1< Size > &terminal_res, utility::vector1< Size > const &working_res, utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model)
void	core::import_pose::update_jump_res (utility::vector1< Size > &jump_res, utility::vector1< Size > const &extra_minimize_jump_res)
void	core::import_pose::add_block_stack_variants (vector1< pose::Pose * > const &pose_pointers, vector1< vector1< Size > > const &pose_res_lists, vector1< Size > const &block_stack_above_res, vector1< Size > const &block_stack_below_res)
void	core::import_pose::check_extra_minimize_res_are_input (utility::vector1< core::Size > const &extra_minimize_res, utility::vector1< core::Size > const &input_domain_map)
utility::vector1< Size >	core::import_pose::figure_out_fixed_domain_map (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &extra_minimize_res)
utility::vector1< Size >	core::import_pose::figure_out_dock_domain_map (utility::vector1< Size > &cutpoint_open_in_full_model, utility::vector1< utility::vector1< Size > > const &pose_res_lists, utility::vector1< Size > const &working_res, utility::vector1< Size > const &sample_res, Size const nres)
void	core::import_pose::reorder_pose (pose::Pose &pose, utility::vector1< Size > &res_list)
bool	core::import_pose::just_modeling_RNA (utility::vector1< std::string > const &fasta_files)
void	core::import_pose::initialize_native_and_align_pose (PoseOP &native_pose, PoseOP &align_pose, core::chemical::ResidueTypeSetCOP rsd_set, PoseCOP start_pose)
void	core::import_pose::process_input_file (std::string const &input_file, utility::vector1< pose::PoseOP > &pose_list, bool is_pdb, bool coarse_rna)
bool	core::import_pose::compare_RNA_char (char const char1, char const char2)
bool	core::import_pose::compare_RNA_secstruct (char const char1, char const char2)
std::string const	core::import_pose::convert_based_on_match_type (std::string const &RNA_string, Size const type)
Size	core::import_pose::get_anchor_rsd (pose::Pose const &pose)
bool	core::import_pose::involved_in_phosphate_torsion (std::string atomname)
void	core::import_pose::remove_cutpoint_closed (pose::Pose &pose, Size const i)
void	core::import_pose::remove_cutpoints_closed (pose::Pose &pose)
void	core::import_pose::make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)
void	core::import_pose::make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)

Detailed Description

various functions to construct Pose object(s) from PDB(s)

A temporary copy of the pose_from_pdb code from the demo directory. Will be phased out in favor of file_data routines soon.

Author

Sergey Lyskov

Typedef Documentation

CifFileOP

using CifFileOP = utility::pointer::shared_ptr<CifFile>

CifParserOP

using CifParserOP = utility::pointer::shared_ptr<CifParser>

Function Documentation

TR()

static basic::Tracer TR ( "core.import_pose.util"  )

static